The issue with using culvert nomographs for pipe systems is that you may not fully account for bend losses and any benching in the structures (which would tend to give an HGL lower than expected), and the inlet conditions (eg headwall with wingwalls) won't match in name to what you might find in piped SD systems. (However if you use the nomograph with the Ke equivalent to the condition in the CB/manhole you are okay for that on). Using culvert nomographs you also don't get any "credit" for approach velocities that keeps water moving through the system, which could yield a higher HGL from using culvert nomographs. So , In a straight run of pipe your culvert nomographs would overestimate the HGL elevation. In a system with bends, who knows?
The FHWA manual HEC-22 is the "bible" for analyzing and designing piped storm drain systems. All the charts and nomographs you would need are there, enabling you to account for bend losses, inlet losses, benching/sumps at junctions, plunging flow, etc.
That said, if you are designing a new SD system, often normal flow can be used to size pipes without considering inlet/junction losses. This is valid for systems of moderate or steep slope and no funky junctions. The way to see if this approach is valid should be to size pipes based on normal flow (Manning's eqn). If the flow in a pipe is subcritical or close to pipe full be careful and analyze more closely; supercritical and less than pipe full should be okay. If all your pipes are 2% or greater you will likely be in the second scenario. Flatter systems, systems with manhole channeling to improve hydraulics, and systems with a downstream tailwater require more scrutiny.